MIAMI (CBSMiami) — In a project all but finished, the Army Corps of Engineers has dredged the channels at and leading to Port Miami for nearly two years, but another U.S. government agency says the Corps wreaked environmental havoc in the process.

The deepened channels will allow the port to handle much bigger ships and do a lot a more business. Politicians from President Obama to Governor Rick Scott on down have hailed the dredge as an economic boon. But environmentalists have opposed it from the start, saying it would destroy the sensitive coral reef off Miami Beach.

In a series of letters and emails, the Corps has been slammed by the National Marine Fisheries Service, a part of the National Oceanographic and Atmospheric Administration (NOAA).

In one letter, the agency says damage to the reef “greatly exceeds” projections, perhaps more than ten times over, and “there is no indication the effects will be temporary.”

Environmentalists who fought the dredge feel vindicated.

“The language used by the National Marine Fisheries Service to describe the condition of the reef is very severe and intense language, and we think it accurately depicts what’s going on out there.” said Rachel Silverstein of the organization Miami Waterkeeper. Miami Waterkeeper, the Audubon Society and Sierra Club are among a dozen groups, called the Biscayne Bay Coalition, that fought a losing court battle to block the dredge.

The project saw six million cubic yards of gunk dredged up, much of it dumped on the sensitive living reef – killing it. Never mind that it is – or was – vital habitat for fish and other living things, the reef is a money maker.

“It provides industry in terms of tourism and fishing and diving. It protects the shoreline of Miami Beach that has to deal with a lot of flooding issues,” Silverstein said.

And now a large piece of a reef that some estimate generates six billion dollars a year for South Florida is gone.

“It’s very unlikely this reef is going to recover in any of our lifetimes – if ever,” Silverstein said.

Late Tuesday, the Army Corps of Engineers issued a statement saying it has worked closely with all agencies, including the National Marine Fisheries Service, in preparing for and carrying out the dredge of Miami’s port channels.

“The environmental effects of the Port Miami dredging project are in line with what was expected,” the Corps’ statement said in part.

As environmentalists mourn the damage done by the Port Miami dredging, they are vigorously opposing a dredge proposed for Port Everglades in Fort Lauderdale that they fear will do similar environmental damage.